Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6625-30. doi: 10.1073/pnas.1419895112. Epub 2015 May 4.

Abstract

K-RAS4B (Kirsten rat sarcoma viral oncogene homolog 4B) is a prenylated, membrane-associated GTPase protein that is a critical switch for the propagation of growth factor signaling pathways to diverse effector proteins, including rapidly accelerated fibrosarcoma (RAF) kinases and RAS-related protein guanine nucleotide dissociation stimulator (RALGDS) proteins. Gain-of-function KRAS mutations occur frequently in human cancers and predict poor clinical outcome, whereas germ-line mutations are associated with developmental syndromes. However, it is not known how these mutations affect K-RAS association with biological membranes or whether this impacts signal transduction. Here, we used solution NMR studies of K-RAS4B tethered to nanodiscs to investigate lipid bilayer-anchored K-RAS4B and its interactions with effector protein RAS-binding domains (RBDs). Unexpectedly, we found that the effector-binding region of activated K-RAS4B is occluded by interaction with the membrane in one of the NMR-observable, and thus highly populated, conformational states. Binding of the RAF isoform ARAF and RALGDS RBDs induced marked reorientation of K-RAS4B from the occluded state to RBD-specific effector-bound states. Importantly, we found that two Noonan syndrome-associated mutations, K5N and D153V, which do not affect the GTPase cycle, relieve the occluded orientation by directly altering the electrostatics of two membrane interaction surfaces. Similarly, the most frequent KRAS oncogenic mutation G12D also drives K-RAS4B toward an exposed configuration. Further, the D153V and G12D mutations increase the rate of association of ARAF-RBD with lipid bilayer-tethered K-RAS4B. We revealed a mechanism of K-RAS4B autoinhibition by membrane sequestration of its effector-binding site, which can be disrupted by disease-associated mutations. Stabilizing the autoinhibitory interactions between K-RAS4B and the membrane could be an attractive target for anticancer drug discovery.

Keywords: KRAS; Noonan syndrome; lipid bilayer nanodisc; nuclear magnetic resonance; oncogenic mutation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites / genetics
  • Genes, ras*
  • Humans
  • Lipid Bilayers
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Mutation*
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Proto-Oncogene Proteins p21(ras) / chemistry
  • Proto-Oncogene Proteins p21(ras) / genetics*
  • Proto-Oncogene Proteins p21(ras) / metabolism*
  • Sequence Homology, Amino Acid
  • Signal Transduction
  • Static Electricity
  • ral Guanine Nucleotide Exchange Factor / chemistry
  • ral Guanine Nucleotide Exchange Factor / genetics
  • ral Guanine Nucleotide Exchange Factor / metabolism

Substances

  • Lipid Bilayers
  • ral Guanine Nucleotide Exchange Factor
  • K-Ras4B protein, human
  • Proto-Oncogene Proteins p21(ras)

Associated data

  • PDB/2MSC
  • PDB/2MSD
  • PDB/2MSE